In our earlier work, we compared the global expression profiles of mouse ES cells and trophoblast stem (TS) cells by DNA microarrays. We studied Esg1, one of the genes identified as a gene expressed specifically in ES cells, and found that the gene encodes an RNA-binding protein that binds to many RNA targets. We have also compared the expression profiles of mouse ES cells undergoing neural differentiation in vitro and those of adult neural stem progenitor (NS) cells. The results suggested that ES cells undergoing neural differentiation in vitro recapitulate the development of neural lineages in vivo. We also inferred a set of 4,000 genes, the expression of which increased with neural commitment differentiation; it can be used as a scale for the degree of commitment to neural differentiation. We also carried out global gene expression profiling of mouse embryonic germ (EG) cells and multipotent adult stem cells (MAPCs). [unreadable] [unreadable] During the last year, we have carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. We found that three genes (Zscan4, Whsc2, and Rhox9) showed a spotty expression pattern (spot-in-colony pattern). We also found nine genes that showed a relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). This indicates the presence of heterogeneous cell population in undifferentiated ES cell cultures. We are currently studying the functional role of these genes in ES cells.